7-77913744-C-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000248550.7(PHTF2):c.776+3335C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0594 in 152,204 control chromosomes in the GnomAD database, including 373 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.059 ( 373 hom., cov: 30)
Consequence
PHTF2
ENST00000248550.7 intron
ENST00000248550.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.677
Publications
2 publications found
Genes affected
PHTF2 (HGNC:13411): (putative homeodomain transcription factor 2) Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0815 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHTF2 | NM_001366089.1 | c.776+3335C>A | intron_variant | Intron 8 of 18 | NP_001353018.1 | |||
PHTF2 | NM_001127357.2 | c.674+3335C>A | intron_variant | Intron 7 of 17 | NP_001120829.1 | |||
PHTF2 | NM_001395272.1 | c.674+3335C>A | intron_variant | Intron 8 of 18 | NP_001382201.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0594 AC: 9041AN: 152086Hom.: 373 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
9041
AN:
152086
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0594 AC: 9042AN: 152204Hom.: 373 Cov.: 30 AF XY: 0.0574 AC XY: 4273AN XY: 74424 show subpopulations
GnomAD4 genome
AF:
AC:
9042
AN:
152204
Hom.:
Cov.:
30
AF XY:
AC XY:
4273
AN XY:
74424
show subpopulations
African (AFR)
AF:
AC:
547
AN:
41554
American (AMR)
AF:
AC:
854
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
524
AN:
3466
East Asian (EAS)
AF:
AC:
276
AN:
5174
South Asian (SAS)
AF:
AC:
167
AN:
4822
European-Finnish (FIN)
AF:
AC:
729
AN:
10598
Middle Eastern (MID)
AF:
AC:
25
AN:
294
European-Non Finnish (NFE)
AF:
AC:
5663
AN:
67996
Other (OTH)
AF:
AC:
140
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
438
876
1313
1751
2189
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
108
216
324
432
540
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
187
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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